How to synchronize biological clocks

Journal of Computational Biology

Volumn 16, Issue 2, 2009, Pages 379-393

  Russo, G ^a   Di Bernardo, M ^b  

^a UNIVERSITY OF NAPLES FEDERICO II   (Italy)

^b UNIVERSITY OF BRISTOL   (United Kingdom)

Author keywords

Networks; Synchronization; Synthetic biology

Indexed keywords

ALGORITHM; ARTICLE; BIOLOGICAL RHYTHM; CELL SYNCHRONIZATION; CONTROLLED STUDY; GLYCOLYSIS; NONHUMAN; OSCILLATOR; PRIORITY JOURNAL; SYSTEMS THEORY; VALIDATION STUDY; YEAST CELL;

ALGORITHMS; BIOLOGICAL CLOCKS; CIRCADIAN RHYTHM; COMPUTER SIMULATION; MATHEMATICS; MODELS, BIOLOGICAL; NEURAL NETWORKS (COMPUTER); YEASTS;

EID: 59649130050     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2008.21TT     Document Type: Article

References (33)

1. Bernard, S., Gonza, D., Cajavec, B., et al. 2003. Synchronization-induced rhythmicity of circadian oscillators in the suprachiasmatic nucleus. PLoS Comput. Biol. 3, 667-679.
2. Bier, M., Bakker, B.M., and Westerhoff, H.V. 2000. How yeast cells synchronize their glycolytic oscillations: a perturbation analytic treatment. Biophys. J. 76, 1087-1093.
3. Botero, J.C., and Slotine, J.J. 2006. Examples of synchronization in discrete chaotic systems. Available at: www.citebase.org/abstract?idDoai: arXiv.org:nlin/0609064. Accessed November 30, 2008.
4. Chen, Z., Odstrcil, E.A., Tu, P., et al. 2005. Logic of the yeast metabolic cycle: Temporal compartmentalization of cellular processes clock. Science 18, 1152-1158.
5. Chilov, D., and Fussenegger, M. 2004. Toward construction of a self-sustained clock-like expression system based on the mammalian circadian clock. Biotechnol. Bioeng. 87, 234-242.
6. Chung, S.J., and Slotine, J.J. 2007. Cooperative robot control and concurrent synchronization of Lagrangian systems. Available at: www.citebase.org/abstract?idDoai:arXiv.org:0711.1709. Accessed November 30, 2008.
7. Elowitz, M.B., and Leibler, S. 2000. A synthetic oscillatory network of transcriptional regulators. Nature 403, 335-338.
8. Garcia-Ojalvo, J., Elowitz, M.B., and Strogatz, S.H. 2004. Modeling a synthetic multicellular clock: Repressilators coupled by quorum sensing. Proc. Natl. Acad. Sci. USA 101, 10955-10960.
9. Gerard, L., and Slotine, J.J. 2006. Neuronal networks and controlled symmetries, a generic framework. Available at: www.citebase.org/abstract? idDoai:arXiv.org:q-bio/0612049. Accessed November 30, 2008.
10. Gonze, D., Bernard, S., Waltermann, C., et al. 2005. Spontaneous synchronization of coupled circadian oscillators. Biophys. J. 89, 120-123.
11. Horn, R.A., and Johnson, C.R. 2001. Matrix Analysis, Cambridge University Press, Cambridge, UK.
12. Jouffroy, J., and Slotine, J.J. 2004. Methodologtical remarks on contraction theory. Presented at the CDC 43rd IEEE Conference on Decision and Control.
13. Kiss, I.Z., Rustin, C.G., Kori, H., et al. 2007. Engineering complex dynamical structures: sequential patterns and desynchronization. Science 316, 1886-1889.
14. Kunz, H., and Achermann, P. 2003. Simulation of circadian rhythm generation in the suprachiasmatic nucleus with locally coupled self-sustained oscillators. J. Theoret. Biol. 224, 63-78.
15. Li, C., Chen, L., and Aihara, K. 2006. Synchronization of coupled nonidentical genetic oscillators. Phys. Biol. 3.
16. Li, C., Chen, L., and Aihara, K. 2007. Stochastic synchronization of genetic oscillators networks. MC Syst. Biol. 1.
17. Lohmiller, W., and Slotine, J.J. 1998. On contraction analysis for non-linear systems. Automatica 34, 683-696.
18. McMillen, D., Kopell, N., Hasty, J., et al. 2002. Synchronizing genetic relaxation oscillators by intercell signaling. Proc. Natl. Acad. Sci. USA 99, 673-686.
19. Mirollo, R.E., and Strogatz, S.H. 1990. Synchronization of pulse-coupled biological oscillators. SIAM J. Appl. Math. 50, 1145-1162.
20. Ott, E. 1993. Chaos in Dynamical Systems, Cambridge University Press, Cambridge, UK.
21. Pham, Q.C., Tabareau, N., and Slotine, J.J. n.d. A contraction theory approach to stochastic incremental stability. IEEE Trans. on Automatic Control (in press).
22. Prill, R.J., Iglesias P.A., and Levchenko, A. 2005. Dynamic properties of network motifs contribute to biological network organization. PLoS Biol. 2, 1881-1892.
23. Pye, E.K. 1969. Biochemical mechanisms underlying the methabolic oscillations in yeast. Can. J. Botany 47, 271-285.
24. Russo, G., and di Bernardo, M. n.d. Contraction theory and the master stability function: linking two approaches to study synchronization. IEEE Trans. Circuits Syst. II (in press).
25. Slotine, J.J., Wang, W., and Rifai, K.E. 2004. Contraction analysis of synchronization of nonlinearly coupled oscillators. Presented at the Sixteenth International Symposium on Mathematical Theory of Networks and Systems.
26. Tyson, J.J., Csikasz-Nagy, A., and Novak, B. 2002. The dynamics of cell cycle regulation. Bioessays 24, 1095-1103.
27. Voet, D., and Voet, J.G. 2004. Biochemistry, John Wiley, New York.
28. Wang, R., Chen, L., and Aihara, K. 2006. Synchronizing a multicellular system by external input: an artificial control strategy. Oxford J. 22, 1775-1781.
29. Wang, W., and Slotine, J.J. 2005. On partial contraction analysis for coupled nonlinear oscillators, Biol. Cybernet. 92, 38-53.
30. Winfree, A.T. 2001. The Geometry of Biological Time, 2nd ed, Springer, New York.
31. Yamaguchi, S., Isejima, H., Matsuo, T., et al. 2003. Photic induction of mper1 and mper2 in CRY-deficient mice lacking a biological clock. Science 302, 2531-2534.
32. You, L., Cox, R.S., Weiss, R., et al. 2004. Programmed population control by cell-cell communication and regulated killing. Nature 428, 868-871.
33. Zhou, T., Zhang, J., Yuan, Z., et al. 2007. External stimuli mediate collective rhythms: artificial control strategies. PLoS ONE 3, 1231.